<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
Good morning,</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
I am using a local install of VEP 84. We are leveraging the —flag_pick_allele and —pick_order options. </div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
This is an example of how we are running VEP:</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<p style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;">
perl variant_effect_predictor.pl --offline --flag_pick_allele <span style="background-color: rgb(255, 255, 0);">
-pick_order canonical,rank</span> --merged --dir_cache variant_effect_predictor/cache-dir -i CDH23.1kg.phase3.v5a.EUR.NO-GT.SPLIT-LFT_ALGN.vcf.gz --plugin CADD,whole_genome_SNVs.tsv.gz,InDels.tsv.gz --vcf -o CDH23.1kg.phase3.v5a.EUR.NO-GT.SPLIT-LFT_ALGN.VEP-CADD.vcf
--stats_file CDH23.1kg.phase3.v5a.EUR.NO-GT.SPLIT-LFT_ALGN.VEP-CADD.html —force_overwrite</p>
<p style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;">
<br>
</p>
<p style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;">
<br>
</p>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
I noticed that in annotating some of the variants, it does not seem to select the transcript using my pick order as I would expect. I am assuming that the canonical transcript is defined by: <a href="http://www.ensembl.org/Help/Glossary?id=346">http://www.ensembl.org/Help/Glossary?id=346</a></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
Example Variants:</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<br>
</div>
<div>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
10<span class="Apple-tab-span" style="white-space: pre;"> </span>73558128<span class="Apple-tab-span" style="white-space: pre;">
</span>rs41281334<span class="Apple-tab-span" style="white-space: pre;"> </span>G<span class="Apple-tab-span" style="white-space: pre;">
</span>A<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;">
</span>PASS<span class="Apple-tab-span" style="white-space: pre;"> </span>AC=34;AN=1006</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
10<span class="Apple-tab-span" style="white-space: pre;"> </span>73558886<span class="Apple-tab-span" style="white-space: pre;">
</span>rs4747194<span class="Apple-tab-span" style="white-space: pre;"> </span>G<span class="Apple-tab-span" style="white-space: pre;">
</span>A<span class="Apple-tab-span" style="white-space: pre;"> </span>.<span class="Apple-tab-span" style="white-space: pre;">
</span>PASS<span class="Apple-tab-span" style="white-space: pre;"> </span>AC=280;AN=1006</p>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<br>
</div>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
<br>
</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
The annotation provided for 10:73558128 (rs41281334) is as follows. The picked transcript is <span style="background-color: rgb(255, 255, 0);">NM_022124.5</span> (which is what I expected since it is the canonical transcript according to the UCSC table query,
and had high rank)</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
<br>
</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
<span style="background-color: rgb(255, 255, 0);">A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_022124.5|protein_coding|50/70||||7237|6847|2283|V/I|Gtc/Atc|||1||1||||4.949|0.225802</span></p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_001171934.1|protein_coding|3/22||||444|127|43|V/I|Gtc/Atc|||1||||||4.949|0.225802</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_001171933.1|protein_coding|3/23||||444|127|43|V/I|Gtc/Atc|||1||||||4.949|0.225802</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
A|missense_variant|MODERATE|CDH23|ENSG00000107736|Transcript|ENST00000224721|protein_coding|49/69||||6867|6862|2288|V/I|Gtc/Atc|||1|||HGNC|13733||4.949|0.225802</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CDH23|ENSG00000107736|Transcript|ENST00000475158|processed_transcript|2/21||||383|||||||1|||HGNC|13733||4.949|0.225802</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
A|missense_variant|MODERATE|CDH23|ENSG00000107736|Transcript|ENST00000398788|protein_coding|3/23||||444|127|43|V/I|Gtc/Atc|||1|||HGNC|13733||4.949|0.225802</p>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<br>
</div>
<div><font face="Calibri,sans-serif" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">The annotation provided for 10: </font><span style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px;">73558886 (r</span><font face="Menlo" size="2">s4747194)</font><span style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px;"> is
as follows. The picked transcript is </span><span style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; background-color: rgb(255, 255, 0);">ENST00000398788.</span><font face="Menlo" size="2" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<b>QUESTION: Why was it not canonical transcript </b></font><span style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px;"><b><span style="background-color: rgb(0, 255, 255);">NM_022124.5</span> which has the same rank?</b></span></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<span style="font-family: Menlo; font-size: 11px;"><br>
</span></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<p style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;">
A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_001171934.1|protein_coding|4/22||||670|353|118|R/Q|cGg/cAg|||1||||||21.7|2.866040</p>
<p style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;">
A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_001171933.1|protein_coding|4/23||||670|353|118|R/Q|cGg/cAg|||1||||||21.7|2.866040</p>
<p style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;">
A|missense_variant|MODERATE|CDH23|ENSG00000107736|Transcript|ENST00000224721|protein_coding|50/69||||7093|7088|2363|R/Q|cGg/cAg|||1|||HGNC|13733||21.7|2.866040</p>
<p style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="background-color: rgb(255, 255, 0);">A|missense_variant|MODERATE|CDH23|ENSG00000107736|Transcript|ENST00000398788|protein_coding|4/23||||670|353|118|R/Q|cGg/cAg|||1||1|HGNC|13733||21.7|2.866040</span></p>
<p style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;">
A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CDH23|ENSG00000107736|Transcript|ENST00000475158|processed_transcript|3/21||||609|||||||1|||HGNC|13733||21.7|2.866040</p>
<p style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="background-color: rgb(0, 255, 255);">A|missense_variant|MODERATE|CDH23|64072|Transcript|NM_022124.5|protein_coding|51/70||||7463|7073|2358|R/Q|cGg/cAg|||1||||||21.7|2.866040</span></p>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<br>
</div>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
<br>
</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
Thanks so much for your help. Please let me know if I need to post to an alternate forum.</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
<br>
</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
Ann</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
<br>
</p>
<p style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px; margin: 0px; line-height: normal;">
<br>
</p>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">
<div id="MAC_OUTLOOK_SIGNATURE">
<div><font class="Apple-style-span"><font class="Apple-style-span" face="Calibri" color="#7f007f">Ann Black-Ziegelbein</font></font></div>
<div><font class="Apple-style-span" face="Calibri" color="#7f007f">Senior Application Developer</font></div>
<div><span style="font-family: Calibri; "><font color="#7f007f">Molecular Otolaryngology and Renal Research Laboratories </font></span></div>
<div><span style="font-family: Calibri; "><font color="#7f007f">University of Iowa</font></span></div>
</div>
</div>
</body>
</html>